A 2-D liquid separations/mass mapping method for interlysate comparison of ovarian cancers

A two-dimensional liquid phase separation of proteins from whole cell lysates coupled on-line to an electrospray-ionization time-of-flight (ESI-TOF) mass spectrometer (MS) is used to map the protein content of ovarian surface epithelial cells (OSE) and an ovarian carcinoma-derived cell line (ES2). The two dimensions involve the use of liquid isoelectric focusing as the first phase and nonporous silica reversed-phase HPLC as the second phase of separation. Accurate molecular weight (MW) values are then obtained upon the basis of ESI-TOFMS so that an image of isolectric point (pI) versus MW analogous to 2-D gel electrophoresis is produced. The accurate MW together with the pI fraction and corresponding hydrophobicity (%B) are used to tag each protein so that protein expression can be compared in interlysate studies. Each protein is also identified on the basis of matrix-assisted laser desorption-ionization (MALDI) TOFMS peptide mapping and intact MW so that a standard map is produced against which other cell lines can be compared. Quantitative changes in protein expression are measured in these interlysate comparisons using internal standards in the on-line ESI-TOFMS process. In the ovarian epithelial cell lines under study, it is shown that in the three pI fractions chosen for detailed analysis, over 50 unique proteins can be detected per fraction, of which 40% can be identified from web-based databases. It is also shown that when using an accurate MW to compare proteins in the OSE versus ovarian cancer sample, there are proteins highly expressed in cancer cells but not in normal cells. In addition, many of the proteins in the cancer sample appear to be down-regulated, as compared to the normal cells. This two-dimensional (2-D) liquid/mass mapping method may provide a means of studying proteins in interlysate comparisons not readily available by other methods.